Showing metabocard for L-Xylonic acid (MMDBc0000525)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:44 UTC
Update Date2024-04-30 19:32:48 UTC
Metabolite IDMMDBc0000525
Metabolite Identification
Common NameL-Xylonic acid
Description​L-Xylonic acid, also known as L-xylonate, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. ​L-Xylonic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb2cfd1380>


  Mrv1652305052017402D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  6  0  0  0
  6  7  1  6  0  0  0
  4  5  1  6  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fdb2cfd1380>

HMDB0060256
     RDKit          3D
L-Xylonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.7364   -1.9271    0.5969 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5540   -0.6929    0.5823 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6402    0.1310    0.3748 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2332   -0.1283    0.7781 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1947    1.2442    0.7350 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1844   -0.6848   -0.1747 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4355   -0.2583   -1.4885 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1254   -0.0681    0.2647 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9577    1.3175    0.1937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2824   -0.5298   -0.5870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4468    0.0823   -0.1413 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7908    1.0092    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8796   -0.4347    1.8069 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6191    1.5912   -0.0993 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1654   -1.7809   -0.1892 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0129    0.6416   -1.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2591   -0.3268    1.3297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2842    1.7769    0.9976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1363   -0.3556   -1.6495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080   -1.6184   -0.4319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5463    1.0118   -0.4531 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  1
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fdb2cfd1380>


  Mrv1652305052017402D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  6  0  0  0
  6  7  1  6  0  0  0
  4  5  1  6  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000525

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H](O)[C@@H](O)[C@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m0/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-NUNKFHFFSA-N

> <FORMULA>
C5H10O6

> <MOLECULAR_WEIGHT>
166.1293

> <EXACT_MASS>
166.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.260703661659544

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid

> <ALOGPS_LOGP>
-2.48

> <JCHEM_LOGP>
-2.7794093686666668

> <ALOGPS_LOGS>
0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.393139811550542

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
32.3085

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-xylonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fdb2cfd1380>

HMDB0060256
     RDKit          3D
L-Xylonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.7364   -1.9271    0.5969 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5540   -0.6929    0.5823 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6402    0.1310    0.3748 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2332   -0.1283    0.7781 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1947    1.2442    0.7350 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1844   -0.6848   -0.1747 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4355   -0.2583   -1.4885 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1254   -0.0681    0.2647 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9577    1.3175    0.1937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2824   -0.5298   -0.5870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4468    0.0823   -0.1413 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7908    1.0092    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8796   -0.4347    1.8069 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6191    1.5912   -0.0993 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1654   -1.7809   -0.1892 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0129    0.6416   -1.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2591   -0.3268    1.3297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2842    1.7769    0.9976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1363   -0.3556   -1.6495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080   -1.6184   -0.4319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5463    1.0118   -0.4531 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  1
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
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PDB for #<Metabolite:0x00007fdb2cfd1380>

HEADER    PROTEIN                                 05-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-MAY-20         0                                  
HETATM    1  C   UNK     0      -6.500   0.395   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -7.833  -0.375   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -6.500   1.935   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.166  -0.375   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.166  -1.915   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.832   0.395   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.832   1.935   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.499  -0.375   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.499  -1.915   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.165   0.395   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.169  -0.375   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    8    7                                                  
CONECT    7    6                                                            
CONECT    8    6   10    9                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for #<Metabolite:0x00007fdb2cfd1380>

COMPND    HMDB0060256
HETATM    1  O1  UNL     1       2.736  -1.927   0.597  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.554  -0.693   0.582  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.640   0.131   0.375  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.233  -0.128   0.778  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.195   1.244   0.735  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.184  -0.685  -0.175  1.00  0.00           C  
HETATM    7  O4  UNL     1       0.436  -0.258  -1.488  1.00  0.00           O  
HETATM    8  C4  UNL     1      -1.125  -0.068   0.265  1.00  0.00           C  
HETATM    9  O5  UNL     1      -0.958   1.318   0.194  1.00  0.00           O  
HETATM   10  C5  UNL     1      -2.282  -0.530  -0.587  1.00  0.00           C  
HETATM   11  O6  UNL     1      -3.447   0.082  -0.141  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.791   1.009   0.871  1.00  0.00           H  
HETATM   13  H2  UNL     1       0.880  -0.435   1.807  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.619   1.591  -0.099  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.165  -1.781  -0.189  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.013   0.642  -1.594  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.259  -0.327   1.330  1.00  0.00           H  
HETATM   18  H7  UNL     1      -1.284   1.777   0.998  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.136  -0.356  -1.649  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.408  -1.618  -0.432  1.00  0.00           H  
HETATM   21  H10 UNL     1      -3.546   1.012  -0.453  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    6   13
CONECT    5   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   19   20
CONECT   11   21
END
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SMILES for #<Metabolite:0x00007fdb2cfd1380>

OC[C@H](O)[C@@H](O)[C@H](O)C(O)=O
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INCHI for #<Metabolite:0x00007fdb2cfd1380>

InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m0/s1
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Synonyms
ValueSource
L-XylonateChEBI
L-Xylonic acidKegg
​L-xylonateGenerator
2,3,4,5-Tetrahydroxypentanoic acidHMDB
XylonateHMDB
Xylonic acidHMDB
D-Xylonic acidMeSH
Molecular FormulaC5H10O6
Average Mass166.1293
Monoisotopic Mass166.047738052
IUPAC Name(2S,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid
Traditional NameL-xylonic acid
CAS Registry NumberNot Available
SMILES
OC[C@H](O)[C@@H](O)[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m0/s1
InChI KeyQXKAIJAYHKCRRA-NUNKFHFFSA-N